FMO DATABASE

FMODB ID: 76Z1K

Calculation Name: 2DST-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DST

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SI36

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-988553.855411
FMO2-HF: Nuclear repulsion	943095.259699
FMO2-HF: Total energy	-45458.595712
FMO2-MP2: Total energy	-45593.043111

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ARG)

Summations of interaction energy for fragment #1(A:2:ARG)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-208.259	-201.465	28.576	-15.657	-19.712	-0.141

Interaction energy analysis for fragmet #1(A:2:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.882 / q_NPA : 0.934

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	4	ALA	0	0.089	0.044	3.884	-1.361	0.544	-0.017	-0.971	-0.918	0.004
4	A	5	GLY	0	-0.057	-0.028	6.134	1.994	1.994	0.000	0.000	0.000	0.000
5	A	6	TYR	0	-0.017	-0.009	9.267	-0.547	-0.547	0.000	0.000	0.000	0.000
6	A	7	LEU	0	0.011	0.008	12.381	0.524	0.524	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.058	-0.023	15.409	0.362	0.362	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.017	-0.009	18.063	0.336	0.336	0.000	0.000	0.000	0.000
9	A	10	TYR	0	-0.020	-0.018	20.376	0.095	0.095	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.031	0.026	23.320	0.237	0.237	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.026	-0.004	19.648	0.109	0.109	0.000	0.000	0.000	0.000
12	A	13	ASN	0	0.016	0.006	16.639	0.145	0.145	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.014	0.012	12.337	-0.583	-0.583	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.021	0.003	9.258	-0.261	-0.261	0.000	0.000	0.000	0.000
15	A	16	PHE	0	-0.021	-0.012	7.460	-0.493	-0.493	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.783	-0.869	2.370	-46.396	-45.730	0.613	-0.322	-0.956	-0.002
17	A	18	ARG	1	0.799	0.902	3.966	26.891	27.283	0.001	-0.086	-0.307	0.000
18	A	19	VAL	0	0.009	-0.011	2.204	-5.518	-2.665	3.768	-2.881	-3.740	-0.019
19	A	20	GLY	0	0.078	0.057	3.778	1.209	1.363	0.011	-0.067	-0.098	0.000
20	A	21	LYS	1	0.915	0.944	7.303	20.084	20.084	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.056	0.039	10.752	0.111	0.111	0.000	0.000	0.000	0.000
22	A	23	PRO	0	0.024	0.007	13.596	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.022	0.008	12.528	-1.552	-1.552	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.014	-0.006	10.868	0.996	0.996	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.011	-0.008	10.330	-2.161	-2.161	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.030	-0.008	5.773	0.255	0.255	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.029	0.003	8.692	-1.306	-1.306	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.046	0.011	8.864	0.796	0.796	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.756	-0.862	10.826	-22.119	-22.119	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.838	-0.906	7.980	-32.442	-32.442	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.022	0.013	3.855	-1.821	-1.692	-0.001	-0.018	-0.110	0.000
32	A	33	SER	0	-0.069	-0.056	3.329	-14.239	-13.534	0.019	-0.324	-0.400	-0.002
33	A	34	ARG	1	0.802	0.899	5.014	25.339	25.396	-0.001	0.000	-0.055	0.000
34	A	35	TRP	0	-0.015	0.002	3.124	4.807	5.903	0.019	-0.522	-0.593	-0.002
35	A	36	PRO	0	0.027	0.021	1.809	-51.719	-57.320	18.621	-7.294	-5.726	-0.093
36	A	37	GLU	-1	-0.703	-0.818	3.092	-48.432	-47.382	0.166	-0.407	-0.809	-0.003
37	A	38	ALA	0	0.001	-0.010	2.253	-24.246	-22.734	2.062	-1.667	-1.907	-0.026
38	A	39	LEU	0	-0.064	-0.028	2.602	6.559	8.222	0.571	-0.529	-1.705	0.003
39	A	40	PRO	0	-0.013	0.012	4.922	2.246	2.278	-0.001	-0.001	-0.030	0.000
40	A	41	GLU	-1	-0.919	-0.970	8.637	-22.617	-22.617	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.005	-0.004	10.898	0.694	0.694	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.012	-0.002	10.184	1.316	1.316	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.090	-0.048	8.949	-1.225	-1.225	0.000	0.000	0.000	0.000
44	A	45	PHE	0	0.078	0.033	5.673	0.303	0.303	0.000	0.000	0.000	0.000
45	A	46	TYR	0	-0.005	-0.019	6.613	-0.913	-0.913	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.016	0.003	2.566	0.020	0.201	2.745	-0.568	-2.358	-0.001
47	A	48	LEU	0	0.007	-0.002	6.703	0.471	0.471	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.730	-0.823	8.342	-32.768	-32.768	0.000	0.000	0.000	0.000
49	A	50	LEU	0	0.008	0.022	10.784	1.946	1.946	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.013	-0.014	14.271	-0.062	-0.062	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.014	0.036	17.458	0.418	0.418	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.031	-0.022	13.356	0.748	0.748	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.026	0.008	10.913	-0.563	-0.563	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.717	0.798	5.883	36.355	36.355	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.027	-0.015	13.001	0.913	0.913	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.930	-0.956	15.089	-13.604	-13.604	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.024	-0.004	18.693	0.118	0.118	0.000	0.000	0.000	0.000
58	A	59	PRO	0	-0.024	0.001	20.840	-0.084	-0.084	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.842	0.903	17.722	15.349	15.349	0.000	0.000	0.000	0.000
60	A	61	MET	0	-0.025	-0.005	21.475	0.336	0.336	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.019	0.010	22.007	-0.445	-0.445	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.016	-0.005	20.718	-0.394	-0.394	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.812	-0.920	21.400	-12.578	-12.578	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.877	-0.935	23.672	-12.104	-12.104	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.020	-0.014	17.703	-0.449	-0.449	0.000	0.000	0.000	0.000
66	A	67	ALA	0	0.009	0.002	18.892	-0.781	-0.781	0.000	0.000	0.000	0.000
67	A	68	HIS	0	0.048	0.014	20.323	-0.368	-0.368	0.000	0.000	0.000	0.000
68	A	69	PHE	0	-0.002	-0.003	18.224	-0.068	-0.068	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.007	0.001	15.214	-0.519	-0.519	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.008	0.003	17.595	-0.338	-0.338	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.013	0.004	20.593	0.219	0.219	0.000	0.000	0.000	0.000
72	A	73	PHE	0	0.004	-0.013	11.294	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.001	-0.004	16.740	-0.162	-0.162	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.010	0.002	17.742	0.159	0.159	0.000	0.000	0.000	0.000
75	A	76	MET	0	-0.017	-0.003	18.748	0.410	0.410	0.000	0.000	0.000	0.000
76	A	77	MET	0	-0.044	-0.019	11.774	0.205	0.205	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.071	-0.036	15.990	0.037	0.037	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.025	-0.009	13.303	-0.207	-0.207	0.000	0.000	0.000	0.000
79	A	80	GLY	0	-0.008	-0.004	17.068	-0.037	-0.037	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.002	-0.005	20.071	0.260	0.260	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.037	0.002	15.012	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.023	-0.001	15.667	0.233	0.233	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.002	-0.003	13.875	-1.454	-1.454	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.001	0.002	9.758	1.001	1.001	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.050	-0.023	11.471	-1.365	-1.365	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.775	0.848	6.101	35.516	35.516	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.022	-0.013	11.942	-0.158	-0.158	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.045	-0.026	13.769	1.161	1.161	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.022	0.012	13.575	0.933	0.933	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.032	-0.020	14.535	0.959	0.959	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.006	-0.002	16.978	0.866	0.866	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.019	-0.004	15.899	0.708	0.708	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.024	0.010	19.181	0.379	0.379	0.000	0.000	0.000	0.000
94	A	95	PRO	0	-0.009	-0.017	20.027	0.233	0.233	0.000	0.000	0.000	0.000
95	A	96	HIS	0	0.039	0.028	22.586	0.466	0.466	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.012	-0.009	17.070	0.133	0.133	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.818	-0.890	21.519	-13.617	-13.617	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.041	-0.013	23.865	0.421	0.421	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.042	-0.017	22.985	0.348	0.348	0.000	0.000	0.000	0.000
100	A	101	GLY	0	-0.011	0.005	24.956	0.065	0.065	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.040	-0.010	18.301	-0.066	-0.066	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.790	0.881	19.815	13.542	13.542	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.005	0.011	17.534	-1.151	-1.151	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.033	-0.024	15.097	0.835	0.835	0.000	0.000	0.000	0.000
105	A	106	PRO	0	-0.010	0.005	14.435	-1.486	-1.486	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.041	0.008	10.566	0.412	0.412	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.836	-0.908	11.149	-24.081	-24.081	0.000	0.000	0.000	0.000
108	A	109	GLY	0	-0.014	-0.005	12.438	-0.753	-0.753	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.024	-0.003	12.222	0.643	0.643	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.874	-0.936	7.951	-33.649	-33.649	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.015	-0.026	6.667	2.711	2.711	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.005	0.002	8.629	2.328	2.328	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.878	-0.914	10.209	-16.916	-16.916	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.001	0.005	11.904	1.702	1.702	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.015	-0.011	10.901	1.618	1.618	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.013	-0.022	14.120	1.716	1.716	0.000	0.000	0.000	0.000
117	A	118	SER	0	0.019	0.002	16.123	1.547	1.547	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.883	0.944	17.416	15.822	15.822	0.000	0.000	0.000	0.000
119	A	120	LEU	0	-0.058	-0.030	16.505	0.660	0.660	0.000	0.000	0.000	0.000
120	A	121	SER	0	-0.033	-0.009	19.639	0.683	0.683	0.000	0.000	0.000	0.000
121	A	122	TYR	0	-0.020	0.000	20.042	0.877	0.877	0.000	0.000	0.000	0.000
122	A	123	GLY	0	-0.053	-0.020	23.859	0.144	0.144	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ARG)